There is always at least one pharmacy (yakkyoku) near or inside every hospital and clinic, where you can go to get any medicine that the doctor prescribes. These usually have similar opening times to hospitals and clinics.
Pharmacies and supermarkets also sell a wide range of medicines for minor ailments that do not require prescriptions. But unless you speak Japanese, you will probably find it difficult to choose them on your own. The best plan is to find a pharmacist who speaks English, or go with someone who speaks Japanese.
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